Question: How to convert from a .txt to a .maf file?
0
gravatar for ksanchez1296
12 months ago by
ksanchez12960 wrote:

I have created a mutation annotation format (maf)-like text file and need to convert it into a .maf file for further analysis. Is there any way to do this conversion using a software or in R? There doesn't seem to be much information going from a .txt -> .maf. Any help would be greatly appreciated! I'm at a roadblock until I can figure this out.

bioinformatics txt tcga R maf • 891 views
ADD COMMENTlink modified 12 months ago by Kevin Blighe41k • written 12 months ago by ksanchez12960
1
gravatar for Kevin Blighe
12 months ago by
Kevin Blighe41k
Kevin Blighe41k wrote:

Your TXT file may already fit the MAF format specification if you have the required columns. You have not indicated the columns that you already have, so, I (and no-one else) can say for definite. Keep in mind that MAF files are plain text, tab-delimited, and have specific column names. The TXT extension itself usually indicates that a file is plain text but says nothing about the structure / arrangement of the data inside.

You can check here whether or not your file is already in the MAF format (see Table 1): Mutation Annotation Format (MAF) Specification

On that same page, see the information under the heading 'MAF file checks'.

Keep further in mind that the MAF format was created as a result of the TCGA project, so, it is tailoured for cancer.

Kevin

ADD COMMENTlink written 12 months ago by Kevin Blighe41k

There is also a different MAF format that predates MAF you are referring to.

ADD REPLYlink written 12 months ago by genomax65k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1859 users visited in the last hour